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The feds slapped the lead contractor on the MTA’s sprawling East Side Access project with 11 “serious” safety violations following a probe into a runway rail car that left two workers injured.

Dragados USA-Judlau JV was hit with $48,000 in fines after an inspection by the Occupational Safety and Health Administration, the government’s workplace- watchdog wing.

It has 15 days to appeal OSHA’s findings.

The inspection was prompted by an Oct. 15 accident at the $7.3 billion project to extend LIRR service to Grand Central Terminal — the largest infrastructure project in the country — in which an unsecured rail car went flying into an aerial lift.

One of the workers suffered broken ribs and a fractured facial bone. The other escaped with minor injuries.

The wheels of the runaway train were not chocked, and it lacked a safety chain, which would have prevented it from rolling off, OSHA found.

In addition, the rail car had no lights to warn workers that it was coming toward them, and those in the aerial lift didn’t have radios to alert them to dangers.

The MTA said it is “working with the contractor to address the issues raised by OSHA.”

Last year, a worker on the site was killed when hit by falling debris.